Re: [AMBER] how to convert (psf) to (prmtop) and (incprd)

From: David A Case <>
Date: Fri, 11 Dec 2020 09:08:52 -0500

On Fri, Dec 11, 2020, Pinky Mazumder wrote:
>How can I convert (.psf) file into (.prmtop) and (incprd) to run simulation
>in AMBER? I have made a cellulose bundle using a cellulose-builder. But
>this provides output as (.pdb) and (.psf) file? But, to perform simulation
>in AMBER, I need topology (.prmtop) and coordinates (.incprd) file.

You have several options. I'm guessing you should try them in the
following order:

1. Use the chamber option in parmed (type 'help chamber' for info.)

2. See if the CHARMM-GUI likes the pdb file, and ask it to create
     Amber inputs. Unlike option #1, this will get you the Amber force
     field, not the CHARMM force field running in Amber.

3. Forget the .psf file, and build the system from the .pdb file using
     tleap. This is likely to be the most difficult path, but you will
     gain lots of useful experience about how Amber works, and will have
     the most control over exactly what you get.


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Received on Fri Dec 11 2020 - 06:30:03 PST
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